EDIT: if you understand effective genome size as "mappable" genome size, than Devon is right, of course.
Assemblies only will provide you with a good size estimate if they are of really high quality. This is usually only the case for either model organisms or small, bacterial genomes.
Assemblies of larger genomes such as plant, animals etc., and in particular draft genomes usually do not contain a complete representation of a single haplogenome - which you would need to get your size estimate right. The reasons are that assembly algorithms usually cannot resolve all repeats and centromeric/telomeric regions, and also are prone to generate multiple sequences for different alleles of the the same region.
In my opinion, there are two better approaches:
1) Use the experimentally determined nuclear DNA (e.g. www.genomesize.com) content to calculate the haploid genome size. DNA content in pg can be directly converted into a bp estimate.
2) Use a k-mer based approaches to estimate the genome sizes form a high coverage NGS data set of your organism